Assembly Name: uagpf v2.0
General Information
Organism: Pinus pinaster
Tissue: several
Description: 1 Material Six tissue samples from Pinus pinaster, labeled 4I1, 4I2, 4I3, 9I1, 9I2 and 9I3, delivered on dry ice. 2 Isolation of total RNA and Analysis The tissues were ground under liquid nitrogen. From the tissue powders total RNA was isolated using the mirVana miRNA isolation kit (Ambion). The total RNA preparations were analyzed for their integrity by capillary electrophoresis. 3 cDNA synthesis The RNAs were pooled in equal amounts. From the RNA pool poly(A)+ RNA was prepared which was used for cDNA synthesis. First-strand cDNA synthesis was primed with a N6 randomized primer. Then 454 adapters A and B were ligated to the 5' and 3' ends of the cDNA. The cDNA was finally amplified with PCR (18 cycles) using a proof reading enzyme 4 Normalization Normalization was carried out by one cycle of denaturation and reassociation of the cDNA, resulting in N1-cDNAs. Reassociated ds-cDNA was separated from the remaining ss-cDNA (normalized cDNA) by passing the mixture over a hydroxylapatite column. After hydroxylapatite chromatography, the ss-cDNA was amplified with 11 PCR cycles. 5 Gel fractionation For Titanium sequencing the cDNA in the size range of 500 – 800 bp was eluted from a preparative agarose gel. An aliquot of the size fractionated cDNA was analyzed by capillary electrophoresis.
Assembly Statistics
Number of used reads: 617972
Number of unigenes: 56229
Mean contig length: 474
SNPs statistics
Tot. SNPs: 753590
Unigenes with SNPs: 29801
Mean SNPs per unigene: 25.2
SSRs statistics
Tot. SSRs: 2805
Mean SSRs per unigene: 1.1
SSRs di-nucl. : 223
SSRs tri-nucl. : 1566
SSRs > tri-nucl. : 1016
Annotations statistics
Annotated unigenes: 44783
Descriptions: 25202
Gos: 3919
Interpros: 5008
ECs: 839
Keggs: 146
Project components

Assembly components:

Unigenes file: uagpf_v2.0_unigenes.fasta

ACE file: uagpf_v2.0.ace

Download annotations for specified unigenes:

Paste your unigenes names list (one unigene per line):
Maximum 10 000 names

Or upload unigenes file with names list (one unigene per line):

File 1: Not available Not available

SeqTrimNext reports:

File 1: augpf_v2.0_report.pdf

Biología Molecular y Biotecnología de Plantas, Facultad de Ciencias y Plataforma Andaluza de Bioinformática, Universidad de Málaga, E-29071 Málaga, Spain